I think this fact could be a result of natural competition between phytoplankton species. Even eutrophic environments could show symptoms of nitrogen limitation (low N:P ratios) and nitrogen-fixing cyanobacteria could proliferate by this time.

I would recommend the study by Rao and Charette (2012): They found benthic N-fixation in an eutrophic estuary as well and suggested an efficient removal of fixed N to cause N-limitation resulting in favorable conditions for diazotrophs.

Few species of Cyanotheceae and Synechococcus can fix nitrogen @ nitrogen availability also. usually unicellular cyanobacteria in the estuary forms large colony surrounded by thick mucilage layer, which make a lower nutrient availability and light to the inner cells of the colony. so those cells of each colony started to form thick wall cells like heterocyst, and fix nitrogen to enrich the nutrient of nearby cells.

there may be other reasons, you may follow the following paper as a reference :

http://www.nature.com/nature/journal/v323/n6090/abs/323720a0.html

Thank you all for the valuable comments

Well its a known fact that cyanobacteria can fix nitrogen. But in eutrophic waterbodies they have to compete with other algal species to bloom. At this stage, cyanobacteria can not risk to loose their energy in Nitrogen fixation, rather they use the available nitrogen source to increase their biomass rapidly.

Nitrogen fixation occurs in all system from freshwater to marine. The presence of certain genes  (nif h d and k generally) in the organism perform this conversion. there are certain pico forms which have these genes can perform nitrogen fixation even if it is not limited by N. these forms may be autotrophic and heterotrophic in forms even if we dont get heterocystic form still there are present  these forms.